abstract：:Tumor mutational burden correlates with response to immune checkpoint blockade in multiple solid tumors, although in microsatellite-stable tumors this association is of uncertain clinical utility. Here we uniformly analyzed whole-exome sequencing (WES) of 249 tumors and matched normal tissue from patients with clinica...

journal_title：Nature genetics

authors： Miao D,Margolis CA,Vokes NI,Liu D,Taylor-Weiner A,Wankowicz SM,Adeegbe D,Keliher D,Schilling B,Tracy A,Manos M,Chau NG,Hanna GJ,Polak P,Rodig SJ,Signoretti S,Sholl LM,Engelman JA,Getz G,Jänne PA,Haddad RI,Chouei

更新日期：2018-09-01 00:00:00

abstract：:In the HTML version of this article initially published, the name of author Diletta Di Mitri was miscoded in the XML such that Di was included as part of the given name instead of the family name. The error has been corrected in the HTML version of the article. ...

journal_title：Nature genetics

authors： Chen J,Guccini I,Di Mitri D,Brina D,Revandkar A,Sarti M,Pasquini E,Alajati A,Pinton S,Losa M,Civenni G,Catapano CV,Sgrignani J,Cavalli A,D'Antuono R,Asara JM,Morandi A,Chiarugi P,Crotti S,Agostini M,Montopoli M,

更新日期：2018-09-01 00:00:00

abstract：:Key challenges for human genetics, precision medicine and evolutionary biology include deciphering the regulatory code of gene expression and understanding the transcriptional effects of genome variation. However, this is extremely difficult because of the enormous scale of the noncoding mutation space. We developed a...

journal_title：Nature genetics

authors： Zhou J,Theesfeld CL,Yao K,Chen KM,Wong AK,Troyanskaya OG

更新日期：2018-08-01 00:00:00

abstract：:In the version of this article originally published, a box was misplaced in Fig. 1. The error has been corrected in the HTML and PDF versions of the article. ...

journal_title：Nature genetics

authors： Leitch HG,Hajkova P

更新日期：2018-08-01 00:00:00

abstract：:We apply integrative approaches to expression quantitative loci (eQTLs) from 44 tissues from the Genotype-Tissue Expression project and genome-wide association study data. About 60% of known trait-associated loci are in linkage disequilibrium with a cis-eQTL, over half of which were not found in previous large-scale w...

journal_title：Nature genetics

authors： Gamazon ER,Segrè AV,van de Bunt M,Wen X,Xi HS,Hormozdiari F,Ongen H,Konkashbaev A,Derks EM,Aguet F,Quan J,GTEx Consortium.,Nicolae DL,Eskin E,Kellis M,Getz G,McCarthy MI,Dermitzakis ET,Cox NJ,Ardlie KG

更新日期：2018-07-01 00:00:00

abstract：:The breast cancer risk variants identified in genome-wide association studies explain only a small fraction of the familial relative risk, and the genes responsible for these associations remain largely unknown. To identify novel risk loci and likely causal genes, we performed a transcriptome-wide association study ev...

journal_title：Nature genetics

authors： Wu L,Shi W,Long J,Guo X,Michailidou K,Beesley J,Bolla MK,Shu XO,Lu Y,Cai Q,Al-Ejeh F,Rozali E,Wang Q,Dennis J,Li B,Zeng C,Feng H,Gusev A,Barfield RT,Andrulis IL,Anton-Culver H,Arndt V,Aronson KJ,Auer PL,Ba

更新日期：2018-07-01 00:00:00

abstract：:The human gut microbiome plays a key role in human health 1 , but 16S characterization lacks quantitative functional annotation 2 . The fecal metabolome provides a functional readout of microbial activity and can be used as an intermediate phenotype mediating host-microbiome interactions 3 . In this comprehensive desc...

journal_title：Nature genetics

authors： Zierer J,Jackson MA,Kastenmüller G,Mangino M,Long T,Telenti A,Mohney RP,Small KS,Bell JT,Steves CJ,Valdes AM,Spector TD,Menni C

更新日期：2018-06-01 00:00:00

abstract：:Glaucoma is the leading cause of irreversible blindness globally 1 . Despite its gravity, the disease is frequently undiagnosed in the community 2 . Raised intraocular pressure (IOP) is the most important risk factor for primary open-angle glaucoma (POAG)3,4. Here we present a meta-analysis of 139,555 European partici...

journal_title：Nature genetics

authors： Khawaja AP,Cooke Bailey JN,Wareham NJ,Scott RA,Simcoe M,Igo RP Jr,Song YE,Wojciechowski R,Cheng CY,Khaw PT,Pasquale LR,Haines JL,Foster PJ,Wiggs JL,Hammond CJ,Hysi PG,UK Biobank Eye and Vision Consortium.,NEIGHBORHOOD C

更新日期：2018-06-01 00:00:00

abstract：:In the version of this article originally published, one of the two authors with the name Wei Zhao was omitted from the author list and the affiliations for both authors were assigned to the single Wei Zhao in the author list. In addition, the ORCID for Wei Zhao (Department of Biostatistics and Epidemiology, Perelman ...

journal_title：Nature genetics

authors： Turcot V,Lu Y,Highland HM,Schurmann C,Justice AE,Fine RS,Bradfield JP,Esko T,Giri A,Graff M,Guo X,Hendricks AE,Karaderi T,Lempradl A,Locke AE,Mahajan A,Marouli E,Sivapalaratnam S,Young KL,Alfred T,Feitosa MF,Mas

更新日期：2018-05-01 00:00:00

abstract：:DNA methylation loss occurs frequently in cancer genomes, primarily within lamina-associated, late-replicating regions termed partially methylated domains (PMDs). We profiled 39 diverse primary tumors and 8 matched adjacent tissues using whole-genome bisulfite sequencing (WGBS) and analyzed them alongside 343 addition...

journal_title：Nature genetics

authors： Zhou W,Dinh HQ,Ramjan Z,Weisenberger DJ,Nicolet CM,Shen H,Laird PW,Berman BP

更新日期：2018-04-01 00:00:00

abstract：:We introduce an approach to identify disease-relevant tissues and cell types by analyzing gene expression data together with genome-wide association study (GWAS) summary statistics. Our approach uses stratified linkage disequilibrium (LD) score regression to test whether disease heritability is enriched in regions sur...

journal_title：Nature genetics

authors： Finucane HK,Reshef YA,Anttila V,Slowikowski K,Gusev A,Byrnes A,Gazal S,Loh PR,Lareau C,Shoresh N,Genovese G,Saunders A,Macosko E,Pollack S,Brainstorm Consortium.,Perry JRB,Buenrostro JD,Bernstein BE,Raychaudhuri S,M

更新日期：2018-04-01 00:00:00

abstract：:Clinical measurements can be viewed as useful intermediate phenotypes to promote understanding of complex human diseases. To acquire comprehensive insights into the underlying genetics, here we conducted a genome-wide association study (GWAS) of 58 quantitative traits in 162,255 Japanese individuals. Overall, we ident...

journal_title：Nature genetics

authors： Kanai M,Akiyama M,Takahashi A,Matoba N,Momozawa Y,Ikeda M,Iwata N,Ikegawa S,Hirata M,Matsuda K,Kubo M,Okada Y,Kamatani Y

更新日期：2018-03-01 00:00:00

abstract：:Regulatory variants are often context specific, modulating gene expression in a subset of possible cellular states. Although these genetic effects can play important roles in disease, the molecular mechanisms underlying context specificity are poorly understood. Here, we identified shared quantitative trait loci (QTLs...

journal_title：Nature genetics

authors： Alasoo K,Rodrigues J,Mukhopadhyay S,Knights AJ,Mann AL,Kundu K,HIPSCI Consortium.,Hale C,Dougan G,Gaffney DJ

更新日期：2018-03-01 00:00:00

abstract：:Genome-wide association scans of complex multipartite traits like the human face typically use preselected phenotypic measures. Here we report a data-driven approach to phenotyping facial shape at multiple levels of organization, allowing for an open-ended description of facial variation while preserving statistical p...

journal_title：Nature genetics

authors： Claes P,Roosenboom J,White JD,Swigut T,Sero D,Li J,Lee MK,Zaidi A,Mattern BC,Liebowitz C,Pearson L,González T,Leslie EJ,Carlson JC,Orlova E,Suetens P,Vandermeulen D,Feingold E,Marazita ML,Shaffer JR,Wysocka J,Sh

更新日期：2018-03-01 00:00:00

abstract：:Pioneer transcription factors establish new cell-fate competence by triggering chromatin remodeling. However, many features of pioneer action, such as their kinetics and stability, remain poorly defined. Here, we show that Pax7, by opening a unique repertoire of enhancers, is necessary and sufficient for specification...

journal_title：Nature genetics

authors： Mayran A,Khetchoumian K,Hariri F,Pastinen T,Gauthier Y,Balsalobre A,Drouin J

更新日期：2018-02-01 00:00:00

abstract：:TET enzymes oxidize 5-methylcytosine (5mC) to 5-hydroxymethylcytosine (5hmC), which can lead to DNA demethylation. However, direct connections between TET-mediated DNA demethylation and transcriptional output are difficult to establish owing to challenges in distinguishing global versus locus-specific effects. Here we...

journal_title：Nature genetics

authors： Verma N,Pan H,Doré LC,Shukla A,Li QV,Pelham-Webb B,Teijeiro V,González F,Krivtsov A,Chang CJ,Papapetrou EP,He C,Elemento O,Huangfu D

更新日期：2018-01-01 00:00:00

abstract：:Plants intimately associate with diverse bacteria. Plant-associated bacteria have ostensibly evolved genes that enable them to adapt to plant environments. However, the identities of such genes are mostly unknown, and their functions are poorly characterized. We sequenced 484 genomes of bacterial isolates from roots o...

journal_title：Nature genetics

authors： Levy A,Salas Gonzalez I,Mittelviefhaus M,Clingenpeel S,Herrera Paredes S,Miao J,Wang K,Devescovi G,Stillman K,Monteiro F,Rangel Alvarez B,Lundberg DS,Lu TY,Lebeis S,Jin Z,McDonald M,Klein AP,Feltcher ME,Rio TG,Grant

更新日期：2017-12-18 00:00:00

abstract：:The CRISPR-Cas9 system enables global screens of gene function with high sensitivity and specificity, but off-target effects have been reported for CRISPR guide RNAs targeting genes that are amplified at high copy number. A new study describes a computational approach to correct for this copy number effect, increasing...

journal_title：Nature genetics

authors： Shen JP,Ideker T

更新日期：2017-11-29 00:00:00

abstract：:Perturbations to mammalian SWI/SNF (mSWI/SNF or BAF) complexes contribute to more than 20% of human cancers, with driving roles first identified in malignant rhabdoid tumor, an aggressive pediatric cancer characterized by biallelic inactivation of the core BAF complex subunit SMARCB1 (BAF47). However, the mechanism by...

journal_title：Nature genetics

authors： Nakayama RT,Pulice JL,Valencia AM,McBride MJ,McKenzie ZM,Gillespie MA,Ku WL,Teng M,Cui K,Williams RT,Cassel SH,Qing H,Widmer CJ,Demetri GD,Irizarry RA,Zhao K,Ranish JA,Kadoch C

更新日期：2017-11-01 00:00:00

abstract：:Human-derived tumor models are becoming popular in the context of personalized medicine, but a new study shows that these models could be less representative of primary tumors than previously thought, particularly when using late passages. ...

journal_title：Nature genetics

authors： Villacorta-Martin C,Craig AJ,Villanueva A

更新日期：2017-10-27 00:00:00

abstract：:A major challenge in inflammatory bowel disease (IBD) is the integration of diverse IBD data sets to construct predictive models of IBD. We present a predictive model of the immune component of IBD that informs causal relationships among loci previously linked to IBD through genome-wide association studies (GWAS) usin...

journal_title：Nature genetics

authors： Peters LA,Perrigoue J,Mortha A,Iuga A,Song WM,Neiman EM,Llewellyn SR,Di Narzo A,Kidd BA,Telesco SE,Zhao Y,Stojmirovic A,Sendecki J,Shameer K,Miotto R,Losic B,Shah H,Lee E,Wang M,Faith JJ,Kasarskis A,Brodmerkel C

更新日期：2017-10-01 00:00:00

abstract：:To evaluate the shared genetic etiology of type 2 diabetes (T2D) and coronary heart disease (CHD), we conducted a genome-wide, multi-ancestry study of genetic variation for both diseases in up to 265,678 subjects for T2D and 260,365 subjects for CHD. We identify 16 previously unreported loci for T2D and 1 locus for CH...

journal_title：Nature genetics

authors： Zhao W,Rasheed A,Tikkanen E,Lee JJ,Butterworth AS,Howson JMM,Assimes TL,Chowdhury R,Orho-Melander M,Damrauer S,Small A,Asma S,Imamura M,Yamauch T,Chambers JC,Chen P,Sapkota BR,Shah N,Jabeen S,Surendran P,Lu Y,Zh

更新日期：2017-10-01 00:00:00

abstract：:Copy number variations (CNVs) often include noncoding sequences and putative enhancers, but how these rearrangements induce disease is poorly understood. Here we investigate CNVs involving the regulatory landscape of IHH (encoding Indian hedgehog), which cause multiple, highly localized phenotypes including craniosyno...

journal_title：Nature genetics

authors： Will AJ,Cova G,Osterwalder M,Chan WL,Wittler L,Brieske N,Heinrich V,de Villartay JP,Vingron M,Klopocki E,Visel A,Lupiáñez DG,Mundlos S

更新日期：2017-10-01 00:00:00

abstract：:A new study reports molecular characterization of the GDF5 locus, which is associated with osteoarthritis risk and adult height in humans. This study provides evidence of positive selection for short stature at GDF5 in modern humans, as well as in archaic Neandertals and Denisovans. ...

journal_title：Nature genetics

authors： Lettre G

更新日期：2017-07-27 00:00:00

abstract：:Although several lung cancer susceptibility loci have been identified, much of the heritability for lung cancer remains unexplained. Here 14,803 cases and 12,262 controls of European descent were genotyped on the OncoArray and combined with existing data for an aggregated genome-wide association study (GWAS) analysis ...

journal_title：Nature genetics

authors： McKay JD,Hung RJ,Han Y,Zong X,Carreras-Torres R,Christiani DC,Caporaso NE,Johansson M,Xiao X,Li Y,Byun J,Dunning A,Pooley KA,Qian DC,Ji X,Liu G,Timofeeva MN,Bojesen SE,Wu X,Le Marchand L,Albanes D,Bickeböller H

更新日期：2017-07-01 00:00:00

abstract：:The mammalian TET enzymes catalyze DNA demethylation. While they have been intensely studied as major epigenetic regulators, little is known about their physiological roles and the extent of functional redundancy following embryo implantation. Here we define non-redundant roles for TET1 at an early postimplantation st...

journal_title：Nature genetics

authors： Khoueiry R,Sohni A,Thienpont B,Luo X,Velde JV,Bartoccetti M,Boeckx B,Zwijsen A,Rao A,Lambrechts D,Koh KP

更新日期：2017-07-01 00:00:00

abstract：:Dominant mutations in the MORC2 gene have recently been shown to cause axonal Charcot-Marie-Tooth (CMT) disease, but the cellular function of MORC2 is poorly understood. Here, through a genome-wide CRISPR-Cas9-mediated forward genetic screen, we identified MORC2 as an essential gene required for epigenetic silencing b...

journal_title：Nature genetics

authors： Tchasovnikarova IA,Timms RT,Douse CH,Roberts RC,Dougan G,Kingston RE,Modis Y,Lehner PJ

更新日期：2017-07-01 00:00:00

abstract：:Structural rearrangements have long been recognized as an important source of genetic variation, with implications in phenotypic diversity and disease, yet their detailed evolutionary dynamics remain elusive. Here we use long-read sequencing to generate end-to-end genome assemblies for 12 strains representing major su...

journal_title：Nature genetics

authors： Yue JX,Li J,Aigrain L,Hallin J,Persson K,Oliver K,Bergström A,Coupland P,Warringer J,Lagomarsino MC,Fischer G,Durbin R,Liti G

更新日期：2017-06-01 00:00:00

abstract：:N6-methyldeoxyadenine (6mA) is a noncanonical DNA base modification present at low levels in plant and animal genomes, but its prevalence and association with genome function in other eukaryotic lineages remains poorly understood. Here we report that abundant 6mA is associated with transcriptionally active genes in ea...

journal_title：Nature genetics

authors： Mondo SJ,Dannebaum RO,Kuo RC,Louie KB,Bewick AJ,LaButti K,Haridas S,Kuo A,Salamov A,Ahrendt SR,Lau R,Bowen BP,Lipzen A,Sullivan W,Andreopoulos BB,Clum A,Lindquist E,Daum C,Northen TR,Kunde-Ramamoorthy G,Schmitz RJ

更新日期：2017-06-01 00:00:00

abstract：:The overwhelming number of genetic alterations identified through cancer genome sequencing requires complementary approaches to interpret their significance and interactions. Here we developed a novel whole-body insertional mutagenesis screen in mice, which was designed for the discovery of Pten-cooperating tumor supp...

journal_title：Nature genetics

authors： de la Rosa J,Weber J,Friedrich MJ,Li Y,Rad L,Ponstingl H,Liang Q,de Quirós SB,Noorani I,Metzakopian E,Strong A,Li MA,Astudillo A,Fernández-García MT,Fernández-García MS,Hoffman GJ,Fuente R,Vassiliou GS,Rad R,López-O

更新日期：2017-05-01 00:00:00

abstract：:Genetic studies of complex traits have mainly identified associations with noncoding variants. To further determine the contribution of regulatory variation, we combined whole-genome and transcriptome data for 624 individuals from Sardinia to identify common and rare variants that influence gene expression and splicin...

journal_title：Nature genetics

authors： Pala M,Zappala Z,Marongiu M,Li X,Davis JR,Cusano R,Crobu F,Kukurba KR,Gloudemans MJ,Reinier F,Berutti R,Piras MG,Mulas A,Zoledziewska M,Marongiu M,Sorokin EP,Hess GT,Smith KS,Busonero F,Maschio A,Steri M,Sidore

更新日期：2017-05-01 00:00:00

abstract：:Recent research has uncovered an important role for de novo variation in neurodevelopmental disorders. Using aggregated data from 9,246 families with autism spectrum disorder, intellectual disability, or developmental delay, we found that ∼1/3 of de novo variants are independently present as standing variation in the ...

journal_title：Nature genetics

authors： Kosmicki JA,Samocha KE,Howrigan DP,Sanders SJ,Slowikowski K,Lek M,Karczewski KJ,Cutler DJ,Devlin B,Roeder K,Buxbaum JD,Neale BM,MacArthur DG,Wall DP,Robinson EB,Daly MJ

更新日期：2017-04-01 00:00:00

abstract：:A study of genetic variation in yeast has identified key quantitative trait loci (QTLs) that suppress the effects of variation at multiple other loci. These loci prove essential to accurately modeling yeast growth in response to different environments. ...

journal_title：Nature genetics

authors： Tyler AL,Carter GW

更新日期：2017-03-30 00:00:00

abstract：:Somatic rearrangements contribute to the mutagenized landscape of cancer genomes. Here, we systematically interrogated rearrangements in 560 breast cancers by using a piecewise constant fitting approach. We identified 33 hotspots of large (>100 kb) tandem duplications, a mutational signature associated with homologous...

journal_title：Nature genetics

authors： Glodzik D,Morganella S,Davies H,Simpson PT,Li Y,Zou X,Diez-Perez J,Staaf J,Alexandrov LB,Smid M,Brinkman AB,Rye IH,Russnes H,Raine K,Purdie CA,Lakhani SR,Thompson AM,Birney E,Stunnenberg HG,van de Vijver MJ,Marten

更新日期：2017-03-01 00:00:00

abstract：:Comparative genomic analyses of primary tumors and metastases within individuals with pancreatic cancer have exposed the complex clonal dynamics that underlie the dissemination of cancer cells to distant sites. Recent studies implicate non-genetic mechanisms in this process, particularly fluctuations in chromatin stat...

journal_title：Nature genetics

authors： Vakoc CR,Tuveson DA

更新日期：2017-02-24 00:00:00

abstract：:To further resolve the genetic architecture of the inflammatory bowel diseases ulcerative colitis and Crohn's disease, we sequenced the whole genomes of 4,280 patients at low coverage and compared them to 3,652 previously sequenced population controls across 73.5 million variants. We then imputed from these sequences ...

journal_title：Nature genetics

authors： Luo Y,de Lange KM,Jostins L,Moutsianas L,Randall J,Kennedy NA,Lamb CA,McCarthy S,Ahmad T,Edwards C,Serra EG,Hart A,Hawkey C,Mansfield JC,Mowat C,Newman WG,Nichols S,Pollard M,Satsangi J,Simmons A,Tremelling M,Uh

更新日期：2017-02-01 00:00:00

abstract：:A CRISPR screen conducted in a CD4+ T cell leukemia line has identified host factors required for HIV infection but dispensable for cellular survival. The results highlight sulfation on the HIV co-receptor CCR5 and cellular aggregation as potential targets for therapeutic intervention. ...

journal_title：Nature genetics

authors： Tsui CK,Gupta A,Bassik MC

更新日期：2017-01-31 00:00:00

abstract：:Metastasis is the leading cause of death in people with lung cancer, yet the molecular effectors underlying tumor dissemination remain poorly defined. Through the development of an in vivo spontaneous lung cancer metastasis model, we show that the developmentally regulated transcriptional repressor Capicua (CIC) suppr...

journal_title：Nature genetics

authors： Okimoto RA,Breitenbuecher F,Olivas VR,Wu W,Gini B,Hofree M,Asthana S,Hrustanovic G,Flanagan J,Tulpule A,Blakely CM,Haringsma HJ,Simmons AD,Gowen K,Suh J,Miller VA,Ali S,Schuler M,Bivona TG

更新日期：2017-01-01 00:00:00

abstract：:Despite the clinical significance of balanced chromosomal abnormalities (BCAs), their characterization has largely been restricted to cytogenetic resolution. We explored the landscape of BCAs at nucleotide resolution in 273 subjects with a spectrum of congenital anomalies. Whole-genome sequencing revised 93% of karyot...

journal_title：Nature genetics

authors： Redin C,Brand H,Collins RL,Kammin T,Mitchell E,Hodge JC,Hanscom C,Pillalamarri V,Seabra CM,Abbott MA,Abdul-Rahman OA,Aberg E,Adley R,Alcaraz-Estrada SL,Alkuraya FS,An Y,Anderson MA,Antolik C,Anyane-Yeboa K,Atkin JF

更新日期：2017-01-01 00:00:00

abstract：:A genome-wide study of fasting insulin, HDL cholesterol and triglycerides, designed to depict insulin resistance, identified 53 independent loci associated with a limited capacity to store fat in a healthy way. The increased power of this multitrait approach provides insights into an otherwise difficult-to-grasp pheno...

journal_title：Nature genetics

authors： Heid IM,Winkler TW

更新日期：2016-12-28 00:00:00